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Halfdan Rydbeck
Profile
Expert in applied bioinformatics with 8+ years of experience in providing transparent and reproducible solutions for diverse areas of biological and medical research. Deep knowledge of underlying issues in need of bioinformatics support. Experience includes genetic epidemiology of rare diseases, integrative omics analysis of data from cancer tissue and immune cells, microarray analysis, preprocessing to final analysis of NGS output. The integrative analysis, performed during phd, encompassed, gene expression, copy number variation, promoter methylation and histone occupancy data. Integrative analysis of proteomics, clinical and brain imaging data. Focused on keeping at the forefront of the latest within computational omics analysis. I have emotional intelligence, strong communication skills and am a great teammate. I am dynamic and work very hard to achieve the intended result which has been decided from the start on time. I am not pretentious. I speak my mind and make it safe for others to do so. My collegues say about me that I am hardworking, joyful and problemsolving.
Objective
To further develop my skills in developing reproducible bioinformatics pipelines and contribute to improved insight into cancer development and treatment through the development of supporting computational infrastructure and algorithms. To further develop my knowledge of and skills in applying AI and ML in piplines. To share attained knowledge.
Relevant competences
- Analysis of proteomics data
- Integrative omics analysis
- Pathway and network analysis
- shell, (Python), R, git, Github, Nextflow, Docker
- scientific communication and writing
Research Experience
Researacher bioinformatics
Sahlgrenska ac., Univeristy of Gothenburg
Göteborg, Sweden
2022 - 2020
- Developed a pipeline of rscripts to perform pathway and correlation network analysis of cord blood plasma proteomics data.
- Worked with Rstudio and the R package collections Bioconductor and Tidyverse. Reports where generated with R notebooks and the R package Bookdown. Github and
- GitKraken is used for code version control. Recently applied R packages are DEqMS for differential expression analysis of mass spectrometry data, WGCNA for proteins correlation analysis and ReactomeGSA for pathway analysis
Senior engineer bioinformatics
Norwegian Sequencing Center
University of Oslo, Norway
2017 - 2014
- Set up server infrastructure for NGS data handling. Manged NGS file servers, user access and data delivery.
- Examples of downstream analysis: Blasted an exon sequence against multiple assembled fish genomes to look for systematic loss in phylogeny. Analyzed bacterial methylomes, sequenced with Pacbio in, respect to virulens.
- System setup, user management, data preprocessing, delivery and down stream analysis of Illumina and Pacbio sequence data at the Norwegian DNA sequencing center. Workflow automation with cron and make
Principal engineer
Bioinformatics core facility
Rikshospitalet HF, Norway
2008 - 2007
- Microarray gene expression analysis
Research assistant
Human Genetics division
Children’s Hospital of Philadelphia, USA
2007 - 2006
- Bash and scripting for data wrangling and testing Solar, Plink, TDT, Merlin, STATA, SAS, R
Senior research assistant
Dept. of genetic epidemiology
Nemours Hospital for Children, USA
2005 - 2004
- Used software for genetic linkage and association studies of diseases/syndroms Velocardiofacial Syndrome, ADHD, Neuroblastoma, Osteoporosis, Cornelia de Lange’s syndrome and Myopia • Solar, Plink, TDT, Merlin, STATA, SAS, R
Database coordinator
Human Genetics division
Children’s Hospital of Philadelphia, USA
2004 - 2002
- Manged a database for SNP information Progeny2000
Teaching Experience
Calmness and exitement are essential prerequistes for good teaching and learning
R for reprodicible scientific programming
Software carpentry
Oslo Norway
2018 - 2017
Version controlling with git and github
Software carpentry
Oslo Norway
2018 - 2017
Unix
Software carpentry
Oslo Norway
2018 - 2017
Education
“Halfdan has shown both analytical and technical skilis in his work. He has also shown an ability to work independently and with the eagerness and persistence required for attaining results. I am convinced that Halfdan will be well prepared and suited for works in the biomedical field. Therefore it is a pleasure to recommend him” Professor Dan Röhme, cmb-genetics University of Gothenburg
Halfdan did a “very good job as a senior engineer at NSC and is a responsible and pleasant person to work with” Professor Kjetil Sigurd Jakobssen, founder of Norwegin DNA Sequencing Center
PhD bioinformatics
Medical faculty, University of Oslo
Oslo, Norway
2012 - 2007
- PhD project with thesis title: Integrative epigenome analysis. Scripts developed in R and The Genomic Hyperbrowser was used to study the dependencies and select genes, based on genomic, epigenomic and transcriptomic alterations in samples from osteosarcoma and immune cells. The gene expression, promoter methylation and DNA copy number data were acquired by oligonucleotide microarray technology, and the histone modification data was acquired by technology based on chromatin immune precipitation and next generation sequencing, ChIP-seq.
- Developed and R package for clustering of genomic tracks.
Master of Science in Bioinformatics
Chalmers University of Technology
Gothenburg, Sweden
2001 - 2000
Master of Science in Molecular biology
University of Gothenburg /Uppsala
Göteborg/Uppsala, Sweden
1999 - 1993
Selected Publications, Posters, and Talks
https://www.researchgate.net/profile/Halfdan-Rydbeck; ORCID identification number: 0000-0003-1606-38420000
The proteome signature of cord blood plasma with high hematopoietic stem and progenitor cell count
Stem Cell Research
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2022
- Authored with Anders K.Nilsson, Annika Thorsell, Sofia Frändberg,Helena Barreto Henriksson, Camilla Hesse, Gunnel Hellgren, Pia Lundgren, AnnHellström
ClusTrack: Feature Extraction and Similarity Measures for Clustering of Genome-Wide Data Sets
Plos One
N/A
2015
- Authored with Geir Kjetil Sandve, Egil Ferkingstad and Eivind Hovig
The Genomic HyperBrowser: inferential genomics at the sequence level
Genome biology
N/A
2010
- Authored with Geir K Sandve, Sveinung Gundersen, Ingrid K Glad, Lars Holden, Marit Holden, Knut Liestøl, Trevor Clancy, Egil Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tøstesen, Arnoldo Frigessi & Eivind Hovig
Special competences
References are available on request:
Preprocessing of NGS output
FASTQC, etc
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Downstream analysis of NGS output
Gene centric(DEG), GO and pathway centric, correlation module centric
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Programming
R, shell, Python
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Version control
git,Github
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Languages
Swedish (native)
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English (native)
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Norwegian (good)
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Conference participation
Pedagogic experience
Tutoring PhD students
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